Skin microbiome changes may predict infant eczema and food allergies

The first clues that a baby may develop eczema or food allergies could be hiding in the microscopic organisms living on their skin, according to a study led by researchers in Washington State University’s College of Veterinary Medicine.

Published in the journal Allergy, the study found infants who later developed the conditions showed changes in their skin microbiome long before symptoms appeared. The work could eventually help health care professionals identify at-risk children earlier and develop more personalized approaches to prevention and treatment.

We actually saw skin microbiome changes in infants who hadn’t even been diagnosed with these diseases yet. That was one of the most exciting findings because those changes could potentially be used as biomarkers to help clinicians diagnose disease earlier.”

Zeyang Shen, assistant professor, WSU College of Veterinary Medicine’s School of Molecular Biosciences and one of the study’s lead authors

Since joining the WSU faculty in fall 2025, Shen’s research has focused on the human skin microbiome, which is home to trillions of microorganisms, and its role in health and disease.

His most recent study focused on atopic dermatitis – commonly known as eczema, which can affect up to 20% of children – along with food sensitivities and food allergies. The conditions frequently appear during infancy and are among the earliest stages of the “atopic march,” a progression of allergic diseases that can later include asthma and other allergic conditions.

Shen’s team analyzed more than 1,000 skin swabs from 429 infants. Samples were collected from the infants when they were 2 to 3 months old, before any had been diagnosed with eczema or food allergies, and again at 12 months of age. Participants also underwent assessments for eczema, food sensitization and food allergies.

Using an advanced DNA sequencing technique, researchers were able to identify the microbes living on infants’ skin and their genetic function.

The researchers noted microbial changes that were present in infants who later developed eczema and food allergies, suggesting microbial differences may emerge long before disease presents.

The researchers also found that infants with eczema alone had different skin microbiome profiles than infants who developed eczema alongside food allergies or food sensitization.

In addition, researchers examined mutations in the FLG gene, one of the strongest known genetic risk factors for eczema. The gene helps produce filaggrin, a protein that keeps the skin’s protective barrier intact. Infants with eczema who carried FLG mutations had distinct skin microbiome profiles compared to noncarriers, indicating a potential connection between genetics and the skin microbiome.

The team also found substantial sharing of microbes between mothers and their infants.

“The microbial strains are very much shared between infants and their mothers,” Shen said. “That gives us another layer to this story, suggesting that the people we live around and continuously exchange microbes with could also be contributing to our skin microbiome.”

Shen said future samples will be taken from the children as they age to investigate how early-life microbiome patterns relate to later health outcomes, including asthma and other allergic diseases.

While additional studies are needed, Shen said the initial findings indicate skin microbiome composition could help identify children at risk of skin and allergic conditions before symptoms develop.

“Today, these diseases are diagnosed after symptoms appear,” he said. “If we can validate these microbial signals in other groups of children, they could potentially serve as early biomarkers that help identify disease risk much earlier.”